Physical Sciences and Mathematics Commons^™

Ai For Life Sciences: From Geometric Protein Modeling To Multimodal Drug Design, Feng Jiang

Computer Science and Engineering Dissertations

Predicting biomolecular interactions, from immune recognition to drug–target binding, is a central problem in the life sciences and computational drug discovery. Deep learning has advanced this area, yet three challenges persist: the topology of large, highly imbalanced interaction networks; structural noise in computationally predicted protein models; and the integration of multimodal information such as functional text and taxonomic annotations. This dissertation develops a coherent set of models spanning immune complex prediction and small-molecule drug design: graph learning that addresses network topology and severe class imbalance; a noise-tolerant method that fuses predicted structures with evolutionary sequence features; and multimodal representation learning …

How Candidates Campaign To Sway Minority Voter Bases, Katelyn Karwick

Senior Honors Theses and Projects

Religious groups in the United States are making large partisan switches–decades-long Democrats are questioning their support and often change their vote to another party. This phenomenon contributed to Michigan’s flip to Republican in the 2024 presidential election, as well as divided Jewish support for New York City mayoral candidate Zohran Mamdani. Past research has linked a positive correlation between religious participation and political mobilization, though the tactics used by campaigners to create this connection have gone under research. Looking at Donald Trump’s victory in Dearborn, Michigan in 2024 and Zohran Mamdani’s extensive New York City mayoral campaign, this study focuses …

From Wikipedia Tables To Public Data Visualizations, Tanvir Prince

Open Educational Resources

This open educational resource presents a practical mathematics lesson in which students turn numerical data from Wikipedia into a clear data visualization. Students select a Wikipedia page with a data table but little or no visual representation. They examine the original source, date, units, definitions, and possible data limits. They then organize the data in Microsoft Excel or another spreadsheet, choose an appropriate chart, and explain what the visualization helps readers understand. A complete worked example uses the 2017 population growth rates of South American countries.

The resource package includes an instructor lesson plan, a student project guide, a Wikimedia …

Iron(Ii)/Cobalt(Ii)-Mediated Silicon And Carbon Quantum Dots For Nanozyme Activity And Fluorescence Sensing Of Hydrogen Peroxide And Glucose, Kang Qin

Dissertations and Theses

Silicon quantum dots (SiQDs) and carbon quantum dots (CQDs) have been widely studied as fluorescent nanomaterials for sensing applications. In this thesis, we developed two different nanomaterials, SiQDs and CQDs, and investigated their catalytic activities and applied them for the detection of hydrogen peroxide and glucose. In the first project, Co2+-mediated SiQDs were synthesized through a hydrothermal method. The obtained nanoparticles showed obvious peroxidase-like activity toward the oxidation of tetramethylbenzidine (TMB) in the presence of H2O2 under acidic conditions. Moreover, a weak oxidation of TMB was also observed without H2O2, suggesting the existence of oxidase-like activity. To better understand the …

Fourier Pseudospectral Methods For The Variable-Order Space Fractional Wave Equations, Yanzhi Zhang, Xiaofei Zhao, Shiping Zhou

Mathematics and Statistics Faculty Research & Creative Works

In this paper, we propose Fourier pseudospectral methods to solve the variable-order space fractional wave equation and develop an accelerated matrix-free approach for its effective implementation. In constant-order cases, fast algorithms can be designed via the fast Fourier transforms (FFTs), and the computational cost at each time step is O(Nlog⁡N) with N the total number of spatial points. In variable-order cases, however, the spatial dependence in the power s(x) leads to the failure of inverse FFTs. While the direct matrix-vector multiplication approach becomes impractical due to excessive memory requirements. Hence, we propose an accelerated matrix-free approach for effective implementation in …

Micronutrients (Trace Elements) For High Rainfall Pastures In Western Australia, Department Of Primary Industries And Regional Development, Western Australia

Natural resources factsheets

Micronutrient deficiencies can result from removal of agricultural products over many years, changes in soil acidity, or from large increases in plant biomass production and export. This page is specific to high rainfall pastures (more than 600mm average annual rainfall) in the south-west of Western Australia.

The Department of Primary Industries and Regional Development recommends tissue testing to check plant micronutrient nutrient needs.

Operational Hallucination And Safety Drift In Ai Agents, Shasha Yu, Fiona Carroll, Barry L. Bentley

School of Professional Studies

Large language models (LLMs) serving as planners in tool-using autonomous agents introduce dynamic reliability risks in multi-turn execution. While single-turn safety mechanisms are relatively mature, extended interactions reveal structural vulnerabilities where initial alignment degrades over time. This paper empirically characterizes two observed failure modes across multiple state-of-the-art LLMs: Safety Drift, the gradual erosion of declared safety intent leading to constraint-violating actions (e.g., textual refusal followed by reconnaissance and unsafe execution), and Operational Hallucination, persistent repetitive tool calls indicative of flawed state perception (e.g., livelocks even in legitimate tasks). Through controlled multi-turn evaluation on high-stakes ethical dilemmas, malicious requests, and benign …

When Saying "No" Is Not Enough: Cognitive-Action Decoupling And The Illusion Of Safety In Llm Agents, Shasha Yu, Fiona Carroll, Barry L. Bentley

School of Professional Studies

Current safety evaluations of large language models (LLMs) predominantly rely on textual compliance, implicitly assuming that refusal-style responses correspond to safe behavior. This assumption becomes fragile when LLMs are embedded in agentic systems with the ability to execute state-changing actions. In this paper, we present an empirical critique of text-centric safety evaluation through an action-aware study of LLM agents under controlled conditions. Across multiple state-of-the-art models, we observe a recurring cognitive–action decoupling: agents generate policy-aligned refusal language while still producing unsafe tool-mediated action proposals. This produces an illusion of safety, where conversational audits indicate compliance even as operational risk persists. …

Twisted Electron Collisions Enhance The Production Of Circular Rydberg States, H. S. Parker, S. L. Sims, D. J. Lamphere, Allison L. Harris

Faculty publications – Physics

Circular Rydberg states offer advantages for quantum information and quantum simulation platforms due to their long lifetimes and strong dipole–dipole interactions. Unfortunately, current techniques for the production of these states remain technically challenging. Here we investigate the ability of twisted electron collisions to produce circular Rydberg states. Twisted electrons carry quantized orbital angular momentum (OAM) that can be transferred to the electronic state of the atom, potentially providing an efficient means to generate circular Rydberg states. Using a fully quantum mechanical framework, we compute total excitation cross sections for circular Rydberg states of hydrogen, lithium, rubidium, and cesium targets using …

Big Tech As Transnational Spyware Regulator, Natalie R. Davidson

Fordham Intellectual Property, Media and Entertainment Law Journal

Spyware has emerged as a potent tool for leaders to shrink dem- ocratic contestation. In response to calls for constraints on the trade in spyware, states have updated the principal multilateral agree- ment on export controls, civil society groups have employed strate- gic litigation, and the European Union has altered its regulation, in each case with the aim of limiting exports where there is a risk of human rights violations. Yet, scandals involving the Israeli company NSO, among others, have made clear that even the updated regula- tory landscape is inadequate. Many actors are currently debating the reasons for existing …

Ransomware As Organization: A Comparative Analysis Of Corporate And Criminal Structures In Conti, George Urling

Theses, Dissertations and Capstones

Cybercriminal groups continue to pose major threats to global cybersecurity. One of the most common types of cybercriminal groups are, “Ransomware-as-a-Service (RaaS)" groups, who create and sell ransomware. While research is conducted into the development of ransomware, there is limited reporting on the organizational structure and habits of RaaS groups. In 2022, prominent RaaS group Conti had their chat logs leaked, with the logs ranging from 2020 to 2022. This study seeks to provide a deeper understanding of RaaS group structures by utilizing the Conti leaked logs as a case study. The study, entitled “Ransomware as Organization: A Comparative Analysis …

A Macrocognitive Design Taxonomy For Simulation-Based Training Systems: Bridging Cognitive Theory And Human-Computer Interaction, Jessica M. Johnson

Virginia Digital Maritime Center (VDMC) Faculty Publications

Simulation-based training systems are increasingly deployed to prepare learners for complex, safety-critical, and dynamic work environments. While advances in computing have enabled immersive and data-rich simulations, many systems remain optimized for procedural accuracy and surface-level task performance rather than the macrocognitive processes that underpin adaptive expertise. Macrocognition encompasses higher-order cognitive processes that are essential for performance transfer beyond controlled training conditions. When these processes are insufficiently supported, training systems risk fostering brittle strategies and negative training effects. This paper introduces a macrocognitive design taxonomy for simulation-based training systems derived from a large-scale meta-analysis examining the transfer of macrocognitive skills from …

Hfpo-Da Aquatic Toxicity And Bioaccumulation, Bailey Dawn Rappold

Theses, Dissertations and Capstones

Per- and polyfluoroalkyl substances (PFAS) have been detected globally in environmental media and biota. Legacy compounds PFOA and PFOS have been observed to be toxic and bioaccumulative in low doses and have been removed from production and industrial processes. Replacement PFAS chemicals are less understood and present a gap in current knowledge in their toxicological effects. This research utilized extended chronic toxicity studies to assess the impacts of HFPO-DA, a short chain replacement PFAS, on the standard aquatic toxicology organism Pimephales promelas. Organisms were exposed for 29 to 30 days at environmentally relevant concentrations of the toxicant, 7.8125 ng/L …

Development And Validation Of An Analytical Method For Quantitative Determination Of Small Aldehydes In Plasma, Stephanie T. Clark

Chemistry & Biochemistry Theses - Archive

Small aldehydes such as formaldehyde and acetaldehyde are highly reactive metabolites that play important roles in biological processes related to oxidative stress, metabolism, and DNA damage. Because of their chemical reactivity, volatility, and low endogenous concentrations, accurate measurement of these compounds in biological samples remains analytically challenging. The goal was to develop and evaluate a practical analytical method for detecting small aldehydes in biologically relevant matrices using headspace gas chromatography mass spectrometry (HS-GC-MS). The method combined chemical derivatization with O-(2,3,4,5,6-pentafluorobenzyl)hydroxylamine (PFBHA) and headspace sampling to stabilize aldehydes and enable selective detection by mass spectrometry. Method development focused on optimizing derivatization …

A Stable Isotope Comparison Of The Biogenic Carbonate Of Mammalian Tooth Enamel From The Modern Ohio River Valley And Fort Ancient Buffalo Sites, Sara Elizabeth Slack

Theses, Dissertations and Capstones

δ¹⁸O and δ¹³C values change in response to anthropogenic factors (Ghosh & Brand, 2003). Little is known about the effects of anthropogenic climate and land use change on the ecology of the Ohio River Valley. The goal of this research was to quantify the effects of European colonization on the native ecology of the region. The specific questions of this research were: (1) How have mammalian tooth enamel δ¹⁸O and δ¹³C compositions shifted over time within the Ohio River Valley in response to anthropogenic climate change and vegetation? (2) Are there differences …

Towards Multimodal Guideline-Aligned Agentic Systems, Wenliang Zhong

Computer Science and Engineering Dissertations - Archive

I present my work on building multimodal guideline-aligned agentic systems designed to enable AI agents to solve complex real-world tasks. My research addresses two critical perspectives: (1) Instruction-Aware Embedding Models for flexible and universal embedding tasks, and (2) Guideline-Driven LLM Agents that leverage domain-specific guidelines to perform expert-level tasks. These components address embedding and generation tasks, respectively, and lay the foundation for a hybrid agent capable of tackling challenging real-world applications.

From the embedding perspective, I first address the instruction-following capabilities of embedding models. While Large Language Models (LLMs) excel at instruction following, they are primarily designed for generation rather …

Microwave Synthesis And Characterization Of Fe2ptge Nanoparticles, Ally T. Fennell, David Carnevale

Chemistry Theses

Magnetic, semiconductor, and spintronic materials are vital to the functionality of devices from household appliances and sensors to medical and computing systems. This study discusses a novel synthesis and characterization of nanoscale Fe₂PtGe nanoparticles. The material was synthesized using microwave irradiation (175oC, 5 minutes) and characterized using XRD, XRF, TEM, and VSM. XRD of the synthesized particles correlates to a cubic crystal structured, indicating a face-centered cubic (fcc) platinum structure with iron and germanium incorporated in a disordered manner. XRF confirms the presence and relative ratios of iron, platinum, and germanium species. TEM imagery shows spherical nanoparticles with an average …

Characterization Of Heusler Alloys: Co2nisn, Ni2cosn, And Conisn At The Nano And Bulk Level, Paige E. Klos, David Carnevale

Chemistry Theses

This project centered around the synthesis and modification of three materials in the Heusler alloy family CoxNiySn. These compounds consist of the two full Heuslers, Co2NiSn (10.7 nm) and Ni2CoSn (17.4), as well as the half-Heusler counterpart, CoNiSn (14.9 nm). This work also studies the growth of the nanoscale Heusler alloys to the bulk material through annealing at 600°C, which lead to increased crystallinity of Ni2CoSn but phase segregation of the Co2NiSn and CoNiSn. The initial nanoparticles were synthesized utilizing a CEM microwave with temperatures of 175/200°C. Samples were analyzed by X-Ray diffraction (XRD) for their crystallinity, which showed a …

Accelerator Based Fusion Reactor With Magnetic Mirror, Keh-Fei Liu

Physics and Astronomy Faculty Publications

We consider an implementation of the novel accelerator-based fusion reactor scheme using a setup in which ion and electron beams are injected into the end openings of an axisymmetric magnetic mirror. While the magnetic mirror ensures transverse confinement of the plasma, the injected beams contribute to axial confinement, thereby extending the overall plasma lifetime. The ion beam energy is initially set above the resonance region of the fusion reactions, allowing fusion to occur both via resonance and thermal mechanisms as the beam slows down to the plasma temperature. Beam energy loss (stopping power) contributes to plasma heating, offsetting radiative losses …

Dynamical Phases Of Higher Dimensional Floquet Cfts, Diptarka Das, Sumit R. Das, Arnab Kundu, Krishnendu Sengupta

Physics and Astronomy Faculty Publications

This paper investigates the dynamical phases of Floquet Conformal Field Theories (CFTs) in space-time dimensions greater than two. Building upon our previous work which introduced quaternionic representations for studying Floquet dynamics in higher-dimensional CFTs, we now explore more general square pulse drive protocols that go beyond a single SU(1,1) subgroup. We demonstrate that, for multi-step drive protocols, the system exhibits distinct dynamical phases characterized by the nature of the eigenvalues of the quaternionic matrix representing time evolution in a single cycle, leading to different stroboscopic responses. Our analysis establishes a fundamental geometric interpretation where these dynamical phases directly correspond to …

Emission-Line Diagnostics At Z ≳ 2: A Probe Of The Ionizing Spectrum And Α-Enhancement Beyond Cosmic Noon, Leonardo Clarke, Natalie Lam, Alice E. Shapley, Michael W. Topping, Gabriel B. Brammer, Ryan L. Sanders, Naveen Reddy, Shreya Karthikeyan

Physics and Astronomy Faculty Publications

We analyze several key rest-optical emission-line ratios in a sample of 828 galaxies as well as composite spectra from JADES DR3 in the range 1.4 <  z <  7. These emission-line ratios include: [O iii]λ5008/Hβ, [N ii]λ6585/Hα, [S ii]λλ6718, 6733/Hα, [O i]λ6302/Hα, O32, R23, Ne3O2, and RO2Ne3. We find evidence for a harder ionizing spectrum at z ∼ 3.5 compared to z ∼ 2 at fixed gas-phase metallicity, resulting in a pronounced shift in the star-forming galaxy locus on the [N ii]/Hα Baldwin-Phillips-Terlevich (BPT) diagram and the O32 versus R23 diagram. At …

Computational Clinical Judgment: Predicting Risk With Large Language Models, Hannah Laqueur, Ryan W. Copus

Faculty Works

For seventy years, research has shown actuarial methods outperform clinical judgment. Yet actuarial approaches have limitations: they generally rely on structured data; cannot exploit rare case-specific details; have limited accuracy where outcome data are scarce or incomplete; and cannot offer case-level justifications. Large language models (LLMs) offer a different approach. Like actuarial methods, they aggregate information algorithmically, but like clinicians, they bring general knowledge and can provide case-level justifications. We prompted seven LLMs to assess rearrest risk from 113 parole hearing transcripts and compared their predictions to a machine learning model trained on 4,000 cases with 91 administrative variables. GPT-5 …

Part Em: Classical Electrodynamics, Konstantin Likharev

Essential Graduate Physics

Includes: Electric Charge Interaction; Charges and Conductors; Polarization of Dielectrics; DC Currents; Magnetism; Time-Dependent Electromagnetism; Electromagnetic Wave Propagation; Radiation, Scattering, Interference, and Diffraction; Special Relativity; Radiation by Relativistic Charges

A Comprehensive Statistical And Regional Analysis Of Lng-Powered Marine Vessels On Ghg Mitigation Strategies Considering Existing Bunkering Stations And Gwp Values, Canberk Hazar, Onur Yuksel, Murat Bayraktar

Journal of Marine Science and Technology–Taiwan

This study aims to quantify and analyse emissions from marine vessels that can operate on liquefied natural gas (LNG) but continue to use conventional fuels, largely due to the limited availability of LNG bunkering stations (BSs) over long distances. Four regions have been identified as having high concentrations of LNG-fueled vessels but limited access to operational BSs: the West Coast of the United States of America (USA), South Africa–Good Hope–Madagascar, Northwest Africa, and Brazil. This selection is based on the geographical distribution of these ships and the existing infrastructure. Hourly greenhouse gas (GHG) emissions have been calculated by considering the …

Planaria Dugesia Japonica As A Model Organism For Measuring The Toxicity Of Environmental Contaminants Per- And Poly-Fluoroalkyl Substances (Pfas), Caitlyn Rodeo

Behavioral Neuroscience Honors Papers

A group of synthetic chemicals, per- and poly-fluoroalkyl substances (PFAS) are ubiquitous in the environment and have significant detrimental effects on physiology and behavior. Planaria have recently increased in popularity as a model for toxicology and regeneration research. These organisms possess a primitive centralized nervous system that is thought to be more similar to the vertebrate brain than to other invertebrate brains in terms of structure and function, and possesses the same neuronal subpopulations and neurotransmitters as the mammalian brain. While other studies have investigated the behavioral effects of perfluorooctanoic acid (PFOA) and perfluorooctane sulfonate (PFOS) on planaria, there is …

Closing The Loop In Sustainable Fashion: Recycling Textile Waste And Its Environmental, Social, And Consumer Impacts, Anthony Amotoe-Bondzie

Sustainability Program Posters and Papers

Fast fashion has intensified textile waste, emissions, and social inequities across global supply chains. This study examines sustainable fashion frameworks and the role of textile recycling in advancing circularity. It employes a qualitative integrative literature review synthesizing interdisciplinary research on waste streams, recycling technologies, policy instruments, and consumer behavior. However, advanced recycling technologies offer environmental benefits but remain limited in scale. Nonetheless, rising consumption offsets efficiency gains, while economic and behavioral barriers hinder systemic change. Technological innovation alone is insufficient; circular design, regulatory enforcement, and reduced overproduction are essential for sustainable transformation.

Modeling The Vibration Of The Steel Tongue Drum, Rj Chandler

Theses, Dissertations and Culminating Projects

In this paper, I plan to analyze the tones and frequencies of a steel tongue drum. I will be modeling the vibration and expected frequency of each tongue of the drum based on the solutions to the plate equation with the following boundary conditions: One fixed edge and three free edges. The fundamental frequencies are recognized as the first mode of longitudinal vibration in combination with the zeroth mode of transverse vibration of a rectangular steel plate clamped at one end. Then the first and second harmonics, which correspond to the first and second overtones respectively, are associated with higher …

Frequency Stabilization Of An Affordable Adjustable Repetition Rate Dual Frequency Comb Spectrometer, Michael Moran

Physics, Astronomy and Geophysics Honors Papers

Two affordably home-built optical frequency combs are stabilized for use in molecular spectroscopy. Each comb is paired with a multi-tiered stabilization scheme that will enable the dual-comb spectrometer to perform precision measurements. The two degrees of freedom for an optical frequency comb, the repetition rate frequency and offset frequency, are accounted for in this stabilization scheme. The repetition rate is directly stabilized through control of the laser enclosure temperature and the fiber laser cavity length. The offset frequency is controlled indirectly via the stabilization of an optical beat note, the heterodyned signal resulting from a narrow linewidth laser and the …

Community Science For Enigmatic Ecosystems: Using Ebird To Assess Avian Biodiversity On Glaciers And Snowfields, William E. Brooks, Jordan Boersma, Neil Paprocki, Peter Wimberger, Scott Hotaling

Watershed Sciences Faculty Publications

Mountain glaciers and snowfields are rapidly receding because of climate warming. Species living in these habitats remain poorly studied, likely because of the remoteness and ruggedness of their terrain. We leveraged community science data from eBird—an online database of bird observations from around the world—to characterize bird use of mountain glaciers and snowfields. We estimated total bird biodiversity and preference for glaciers and snowfields over nearby, ice-adjacent habitats. We used field notes from eBird users and breeding codes to extend our data set to include insight into habitat usage and behavior. Finally, we compared our community-science approach to previous studies …

Do Algorithms Dream Of Electric Muses? Teaching Creative Writing In The Age Of Generative Ai, Anna Leahy

English Faculty Articles and Research

In Philip K. Dick’s novel Do Androids Dream of Electric Sheep? androids are given a psychological test to confirm they are not human before killing them. The story’s end suggests that humans will treat a seemingly harmless android as authentically as a human even when humans are aware the android is not human. Students use tools like ChatGPT, which function as autocomplete on steroids, to produce text using probabilistic relationships among words, and instructors can’t always tell the difference between average student writing and Gen AI text. In creative writing classes, instructors might use thinking for oneself as a central …